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It can be asymptomatic, or it can produce a necrotic lesion in the upper digestive tract and spread to other organs, causing the death of the infected birds. In this study, we aimed to evaluate an adapted real-time PCR method for the diagnosis of different genotypes and species of avian oropharyngeal trichomonads. Fifty-six samples from the oropharynx of Bonelli\u2019s eagles (<jats:italic>Aquila fasciata<\/jats:italic>) obtained between 2018 and 2019 were analyzed using the real-time PCR and the end-point PCR, both targeting trichomonads ITS, and the results were compared by a coefficient of agreement. All positive samples were sequenced. The analysis showed a higher percentage of detection of real-time PCR ITS compared with end-point PCR ITS (64.3 vs 55.4%), and good agreement value (Kappa\u2009=\u20090.816). Melting temperature value for resulting amplicons of real-time PCR for avian trichomonads was 83.45\u2009\u00b1\u20090.72\u00a0\u00b0C. Genotypes A, D, and III were found among the sequences. Moreover,<jats:italic>Trichomonas gypaetinii<\/jats:italic>, a common species in scavenger birds, is reported for the first time in Bonelli\u2019s eagles.<\/jats:p>","DOI":"10.1007\/s00436-022-07693-3","type":"journal-article","created":{"date-parts":[[2022,10,19]],"date-time":"2022-10-19T08:02:57Z","timestamp":1666166577000},"page":"3663-3670","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Adaptation of the classical end-point ITS-PCR for the diagnosis of avian trichomonosis to a real-time PCR reveals Bonelli\u2019s eagle as a new host for Trichomonas gypaetinii"],"prefix":"10.1007","volume":"121","author":[{"given":"Sandra","family":"Alejandro Mateo","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Iris","family":"Azami-Conesa","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"B\u00e1rbara","family":"Mart\u00edn-Maldonado","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Natalia","family":"Pastor-Tibur\u00f3n","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Raquel","family":"Mart\u00edn-Hern\u00e1ndez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fernando","family":"Gonz\u00e1lez-Gonz\u00e1lez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mar\u00eda Teresa","family":"G\u00f3mez-Mu\u00f1oz","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2022,10,19]]},"reference":[{"key":"7693_CR1","doi-asserted-by":"publisher","first-page":"234","DOI":"10.1016\/j.meegid.2019.05.007","volume":"73","author":"AF Alrefaei","year":"2019","unstructured":"Alrefaei AF, Gerhold RW, Nader JL, Bell DJ, Tyler KM (2019) Improved subtyping affords better discrimination of Trichomonas gallinae strains and suggests hybrid lineages. 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The research work is compliant with the national regulations on this subject.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent to participate"}},{"value":"Not applicable.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":5,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}